Internship - Computational Biology Unit, University of Bergen   Bergen, Norway
Dahle group
Supervisor: Håkon DAHLE

Investigate the phylogeny of dominating metagenomics assembled genomes from various hydrothermal systems along the Arctic Mid Ocean Ridge.

Analysis of metagenomic samples from the Aurora vent field to retrieve information about potentially novel lineages, microdiversity patterns, and biogeographical patterns.
Retrieval of reference genomes from public databases, extraction of conserved single copy marker genes / proteins from whole genomes.
Construction of multiple sequence alignments of orthologous proteins, alignment trimming, alignment concatenation, and tree-building using maximum-likelihood algorithms.

Apprenticeship - Bioinformatics and Biostatistics Hub, Institut Pasteur   Paris, France
GORE team (Genome Organisation, Regulation and Expression)
Supervisors: Claudia CHICA and Victoire BAILLET

Quantify and assess the regulatory meaning of epigenomic variability by identifying the main sources of variability for different chromatin factors through the integration of multiple data types.

Exploration of various methods for the integration of multiple epigenomic data sets: matrix factorization approaches for dimensionality reduction.
Application of the ICA (Independent Component Analysis) approach to characterise the epigenome's role in the switch from an healthy to a cancerous cell state.
Side project : development of an ATAC-seq pipeline in snake make: definition and implementation of rules, tools benchmark.

Scientific output:   JOBIM 2022 Poster

Internship - Bioinformatics and Biostatistics Hub, Institut Pasteur   Paris, France
GORE team (Genome Organisation, Regulation and Expression)
Supervisors: Claudia CHICA and Victoire BAILLET

Chromatin metaprofiling of healthy and cancer cells using publicly available databases.

Construction of a dataset fitted to answer the question : curation of the EpiMap database and selection of samples of interest.
Assessment of the impact of epigenoøics data's variability on the chromatin states obtained with the tool ChromHMM : comparison of experimentally obtained and imputed samples, in healthy and cancerous cells.

Student job - Chambermaid, Hôtel Neige et Roc   Samoëns, France

Sanitation, affording comfort for tourists and travelers, and ambassador for the hotel and its brand.

Perform cleaning duties to maintain the hotel in a clean and orderly state.
Maintain a professional and sociable demeanor to convey a helpful and friendly attitude towards guests and their requirements.

Internship - MICALIS research group, INRA Jouy-en-Josas   Jouy-en-Josas, France
Phage team
Supervisors: Marie-Agnès PETIT and Olivier INIZAN

Packaging and distribution of Virfam, a tool for bacteriophages classification.

Creation of a downloadable file in OVA format (Open Virtual Appliance) containing the Virfam installer as well as the necessary dependencies, frozen in a Conda environmemt.

C programming tutoring - University of Clermont-Ferrand   Aurillac, France

C programming teaching to first-year students of the bioinformatics technical degree, 2h/week.

Organisation and preparation of weekly tutoring sessions to provide collaborative instruction in C and algorithm basics to first-year students.

Software tester - Rayscan Technologies GmbH   Meersburg, Germany

Implememtation of Unit Tests in C++ with the unit testing framework module CPPUNIT and implementation of Coded UI Tests with AutoIT.

Design and execution of Unit and UI Tests and manual testing of the software on an industrial computer tomography machine.
Preparation of reports on all aspects related to the software testing carried, reported to the design team.
Translation of the user interface from German to English, French and Russian.